Comments (11)
mattwthompson
commented on July 1, 2024
1
Is a downgrade in Cython versions necessary?
Yes, that's the solution
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mattwthompson
commented on July 1, 2024
I wasn't sure if Cython 3 was ever going to come out, but this isn't much of a surprise. I bet there's more code that needs to be updated.
We should definitely pin to version 2 for the time being.
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mattwthompson
commented on July 1, 2024
conda-forge/mdtraj-feedstock#49
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mattwthompson
commented on July 1, 2024
What needs to be done to fix things on the PyPI side of things? I assume updating the TOML file won't impact the sdist that's already released and uploaded?
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jeremyleung521
commented on July 1, 2024
Correct. After the TOML file fix commit, you'll need to push an additional bug fix release to PyPI to fix new installs. It would probably require a new version number (1.9.9 or with 1.9.8.post1, though I've never personally used the post1 thing before).
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vid277
commented on July 1, 2024
Is this error fixed and can it be installed through Pip? Is a downgrade in Cython versions necessary? I am running mdtraj from Google Colab and receiving a similar error.
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mattwthompson
commented on July 1, 2024
This should be resolved with release 1.9.9 - thanks again to @jeremyleung521 for bringing this to our attention and guiding us through to a fix
If there are any deployment issues with that release, please share them here: #1805
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mgorny
commented on July 1, 2024
Could you please reopen the bug, to track support for Cython 3? At this point Cython 0.29* is no longer maintained, and is already facing first bugs related to GCC 14 (not saying mdtraj is affected, I haven't tried, just saying from a wider perspective of a distribution that aims to remove Cython<3 altogether).
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mattwthompson
commented on July 1, 2024
A PR to migrate to Cython 3 would be welcome; for now our builds of existing are working, if that changes we'd have to revisit things
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eli-schwartz
commented on July 1, 2024
Could you please reopen the bug, to track support for Cython 3? At this point Cython 0.29* is no longer maintained, and is already facing first bugs related to GCC 14 (not saying mdtraj is affected, I haven't tried, just saying from a wider perspective of a distribution that aims to remove Cython<3 altogether).
Funnily enough, mdtraj is affected:
x86_64-pc-linux-gnu-gcc -Wsign-compare -DNDEBUG -march=native -fstack-protector-all -O2 -pipe -fdiagnostics-color=always -frecord-gcc-switches -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-clash-protection -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Werror=int-conversion -Werror=incompatible-pointer-types -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.11/site-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_11/temp.linux-x86_64-3.11/mdtraj/formats/tng/src/lib/tng_io.o
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’:
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: error: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Werror=incompatible-pointer-types]
1064 | tng_data->input_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: error: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Werror=incompatible-pointer-types]
1073 | tng_data->input_endianness_swap_func_64 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: error: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Werror=incompatible-pointer-types]
1089 | tng_data->input_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: error: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Werror=incompatible-pointer-types]
1098 | tng_data->input_endianness_swap_func_64 =
| ^
It is just that this particular code isn't a cythonized file.
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sukritsingh
commented on July 1, 2024
Looks like the issues there are related to reading and writing TNG files, which I believe we removed support for with #1788. We may just need to remove that particular block of code and everything else would be fine (with at least what we currently have)
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